2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* mainbase.cpp (Save): QDir::toNativeSeparators(fname). Invoke

	save with format argument set to zero to force QImage to guess the

	format by looking at fileName's suffix.

	* VirtualLeaf-install.nsi: Put uninstaller in top directory.

	* modelcatalogue.cpp (InstallModel): For all OS-es. Move from "bin" directory to root application folder.

	* VirtualLeaf.pro: MAXOSX, look for gpl3.txt in the ../doc directory.

	* Makefile (Makefile.libplugin): Removed -makefile qmake option.

	* VirtualLeaf.cpp (TIMESTEP): Removed getIterations().

	* mesh.h (Mesh): Removed {increment,get}Iterations().

	* canvas.cpp (TimeStepWrap): Replaced getIterations() with getTime().

2010-10-15    <guravage@caterpie.sen.cwi.nl>

	* mesh.h (Mesh): Added iterations. incrementIterations() and

	getIterations().

	* VirtualLeaf.cpp (Plot): Replaced local frame counter with

	mesh.incrementIterations().

	* canvas.cpp (TimeStepWrap): Replaced local counter with

	mesh.incrementIterations().

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Turned debug off to make all profiles must be

	consistant.

	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX

	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the

	uninstaller all go in the bin directory. And leaves directory

	placed under data directory.

	* canvas.cpp (exportCellData): Added a check to inquire before

	overwritting an existing file.

2010-10-14    <merks@cwi.nl>

	* mesh.cpp: In response to referees' comments, added new parameter

	"yield_threshold" instead of fixed parameter '4' for yield

	threshold.

	* wallitem.cpp: when clicking a wall, both the wall type was

	cycled and the transporterdialog popped up. Corrected this - for

	wall type cycling, hold the Control button while left

	clicking. TransporterDialog only pops up for left click. Also made

	sure the wall is redrawn after changing the transporter values.

	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

	* hull.h: added an operator< to sort Points

	* hull.cpp: added an operator< to sort Points

	* cellbase.cpp (ExactCircumference): I added a new function

	ExactCircumference, yielding the circumference of the cell along

	its wall_elements

	* VirtualLeaf.cpp: adjust info_string to accomodate for new name

	of function CellBase::Circumference -> CellBase::WallCircumference

	* mesh.cpp: corrected Mesh::Compactness, the boundary coordinates

	need to be sorted in x,y order for the convex hull algorithm

	(thanks Margriet!). I updated CSVExportCellData so it exports the

	circumferences of hull and boundary_polygon.

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'

	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data

	filename now incorporates iteration number.

	* canvas.h (MainBase): Removed TimeStamp().

2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h:

	* pardialog.cpp:

	* parameter.h:

	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.

	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.

2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* Makefile (Makefile.tutorial3): Removed -makefile qmake option.

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.h (SimPluginInterface): Added default LeafML file.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.pro: Corrected windows library path.

    cerr << endl;

  }

};

double PINSum(Cell &c) {

	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );

}

class DrawCell {

public:

  void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {

    if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {

      if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) 

	if (m.ShowToolTipsP()) {

	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());

	  info_string += "\n" + c.printednodelist();

	  c.Draw(&canvas, info_string);

	} else {

	  c.Draw(&canvas);

	}

      if (m.ShowCentersP())

	c.DrawCenter(&canvas);

    if (m.ShowFluxesP())

	c.DrawFluxes(&canvas, par.arrowsize);

       }

  }

};

Mesh mesh;

bool batch=false;

void MainBase::Plot(int resize_stride) {

  clear();

  static int count=0;

  if (resize_stride) {

    if ( !((++count)%resize_stride) ) {

      FitLeafToCanvas();

    }

  }

  mesh.LoopCells(DrawCell(),canvas,*this);

  if (ShowNodeNumbersP()) 

    mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;

  if (ShowCellNumbersP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;

  if (ShowCellAxesP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );

  if (ShowCellStrainP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );

  if (ShowWallsP())

    mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );

	if (ShowApoplastsP()) 

		mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );

	if (ShowMeshP()) 

    mesh.DrawNodes(&canvas);

  if (ShowBoundaryOnlyP()) 

    mesh.DrawBoundary(&canvas);

	if ( ( batch || MovieFramesP() )) {

		static int frame = 0;

		// frame numbers are sequential for the most frequently written file type.

		// for the less frequently written file type they match the other type

		if (!(count%par.storage_stride) )  {

			stringstream fname;

			fname << par.datadir << "/leaf.";

			fname.fill('0');

			fname.width(6);

			/* 

			 fname << frame << ".pdf";

			if (par.storage_stride <= par.xml_storage_stride) {

				frame++;

			}

			Save(fname.str().c_str(), "PDF");

			*/

			if (par.storage_stride <= par.xml_storage_stride) {

				frame++;

			}

		}

		if (!(count%par.xml_storage_stride)) {

			stringstream fname;

			fname << par.datadir << "/leaf.";

			fname.fill('0');

			fname.width(6);

			fname << frame << ".xml";

			if (par.xml_storage_stride < par.storage_stride) {

				frame++;

			}

			// Write XML file every ten plot steps

			mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());

		}

	}

}

void Cell::Flux(double *flux, double *D)  {

  // loop over cell edges

  for (int c=0;c<Cell::nchem;c++) flux[c]=0.;

  for (list<Wall *>::iterator i=walls.begin();

       i!=walls.end();

       i++) {

    // leaf cannot take up chemicals from environment ("no flux boundary")

    if ((*i)->c2->BoundaryPolP()) continue;

    // flux depends on edge length and concentration difference

    for (int c=0;c<Cell::nchem;c++) {

      double phi = (*i)->length * ( D[c] ) * ( (*i)->c2->chem[c] - chem[c] );

      if ((*i)->c1!=this) {

	cerr << "Warning, bad cells boundary: " << (*i)->c1->index << ", " << index << endl;

      }

      flux[c] += phi;

    }    

  }

}

INIT {

	if (leaffile) { 

    xmlNode *settings;

    mesh.XMLRead(leaffile, &settings);

    main_window->XMLReadSettings(settings);

    xmlFree(settings);

    main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));

  } else {

	  Cell &circle=mesh.CircularCell(0,0,10,10);

    circle.SetTargetArea(circle.CalcArea());

	  mesh.SetBaseArea();

	// clean up chemicals 

	  for (int c=0; c<Cell::NChem(); c++) {

		  circle.SetChemical(c, 0.);

      }

  }

}

TIMESTEP {

  static int i=0;

  static int t=0;

  static int ncells;

  if (!batch) {

    UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);

  }

  ncells=mesh.NCells();

  double dh;

  if(DynamicCellsP()) {

    dh = mesh.DisplaceNodes();

    // Only allow for node insertion, cell division and cell growth

    // if the system has equillibrized

    // i.e. cell wall tension equillibrization is much faster

    // than biological processes, including division, cell wall yielding

    // and cell expansion

#include <QBrush>

#include <QToolTip>

#include "simplugin.h"

#include <QPluginLoader>

#include <QDir>

#include "modelcatalogue.h"

static const std::string _module_id("$Id$");

extern Parameter par;

MainBase *main_window = 0;

#ifdef XFIGGRAPHICS

#define TIMESTEP double Graphics::TimeStep(void)

#endif

class PrintNode {

public:

  void operator() (const Node &n) const 

  {

    cerr << n.Index() << ": " << n <<  endl;

  }

};

class EdgeSource {

public:

  void operator() (Cell &c) {

    if (c.AtBoundaryP()) {

      cerr << "Cell " << c.Index() << " is a source cell.\n";

      c.SetSource(0,par.source);

    } else {

      cerr << "Cell " << c.Index() << " is _not_ a source cell.\n";

    }

  }

};

class CellInfo {

public:

  void operator() (Cell &c,std::ostream &os) const {

    os << "Cell " << c.index << " says: " << endl;

    os << "c.nodes.size() = " << c.nodes.size() << endl;

    for (list<Node *>::iterator i=c.nodes.begin(); i!=c.nodes.end(); i++) {

      cerr << (*i)->Index() << " ";

    }

    cerr << endl;

  }

};

double PINSum(Cell &c) {

  return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );

}

class DrawCell {

public:

  void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {

    if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {

      if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) {

	if (m.ShowToolTipsP()) {

	  //QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());

		QString info_string=QString("Cell %1, chemicals(%2): ").arg(c.Index()).arg(Cell::NChem());

		for (int i=0;i<Cell::NChem();i++) {

			info_string += QString("%1 ").arg(c.Chemical(i));

		}

		info_string += QString("\nArea is %1\n Circumference is %2\n Boundary type is %3").arg(c.Area()).arg(c.WallCircumference()).arg(c.BoundaryStr());

	  info_string += "\nNodes: " + c.printednodelist();

	  c.Draw(&canvas, info_string);

	} else {

	  c.Draw(&canvas);

	}

      }

      if (m.ShowCentersP()){

	c.DrawCenter(&canvas);

      }

      if (m.ShowFluxesP()){

	c.DrawFluxes(&canvas, par.arrowsize);

      }

    }

  }

};

Mesh mesh;

bool batch=false;

void MainBase::Plot(int resize_stride)

{

  clear();

  if (resize_stride) {

    if ( !((count)%resize_stride) ) {

      FitLeafToCanvas();

    }

  }

  mesh.LoopCells(DrawCell(),canvas,*this);

  if (ShowNodeNumbersP()) 

    mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;

  if (ShowCellNumbersP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;

  if (ShowCellAxesP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );

  if (ShowCellStrainP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );

  if (ShowWallsP())

    mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );

/*  if (ShowApoplastsP()) 

    mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );

*/

  if (ShowMeshP()) 

    mesh.DrawNodes(&canvas);

  if (ShowBoundaryOnlyP()) 

    mesh.DrawBoundary(&canvas);

  if ( ( batch || MovieFramesP() )) {

      stringstream fname;

      fname << par.datadir << "/leaf.";

      fname.fill('0');

      fname.width(6);

    }

    if (!(count%par.xml_storage_stride)) {

      stringstream fname;

      fname << par.datadir << "/leaf.";

      fname.fill('0');

      fname.width(6);

      // Write XML file every ten plot steps

      mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());

    }

  }

}

INIT {

  //mesh.SetSimPlugin(plugin);

  if (leaffile) { 

    xmlNode *settings;

    mesh.XMLRead(leaffile, &settings);

    main_window->XMLReadSettings(settings);

    xmlFree(settings);

    main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));

  } else {

    mesh.StandardInit();

  }

  Cell::SetMagnification(1);

  Cell::setOffset(0,0);

  FitLeafToCanvas();

  Plot();

}

TIMESTEP {

  static int i=0;

  static int t=0;

  static int ncells;

  if (!batch) {

    UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);

  }

  ncells=mesh.NCells();

  double dh;

  if(DynamicCellsP()) {

    dh = mesh.DisplaceNodes();

    // Only allow for node insertion, cell division and cell growth

    // if the system has equillibrized

    // i.e. cell wall tension equillibrization is much faster

    // than biological processes, including division, cell wall yielding

    // and cell expansion

    mesh.InsertNodes(); // (this amounts to cell wall yielding)

    if ( (-dh) < par.energy_threshold) {

      mesh.IncreaseCellCapacityIfNecessary();

      mesh.DoCellHouseKeeping();

      //mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division

      // Reaction diffusion	

      mesh.ReactDiffuse(par.rd_dt);

      t++;

      Plot(par.resize_stride);

    }

  } else {

    mesh.ReactDiffuse(par.rd_dt);

    Plot(par.resize_stride);

  }

  i++;

  return mesh.getTime();

}

/* Called if a cell is clicked */

void Cell::OnClick(QMouseEvent *e){}

/* Custom message handler - Default appends a newline character to the end of each line. */ 

void vlMessageOutput(QtMsgType type, const char *msg)

{

  switch (type) {

  case QtDebugMsg:

    //fprintf(stderr, "Debug: %s\n", msg);

    cerr << msg << flush;

    break;

  case QtWarningMsg:

    //fprintf(stderr, "Warning: %s\n", msg);

    cerr << "Warning: " << msg << flush;

    break;

  case QtCriticalMsg:

    fprintf(stderr, "Critical: %s\n", msg);

    cerr << "Critical: " << msg << flush;

    break;

  case QtFatalMsg:

    //fprintf(stderr, "Fatal: %s\n", msg);

    cerr << "Fatal: " << msg << flush;

    abort();

  }

}

void MainBase::XMLReadSettings(xmlNode *settings)

{

  // Many files have no settings section, so don't complain about it.

  // Defaults will be used instead.

  if (settings == 0) {

    return;

  }

  XMLReadViewport(settings);

  xmlNode *cur = settings->xmlChildrenNode;

  while (cur!=NULL) {

    if ((!xmlStrcmp(cur->name, (const xmlChar *)"setting"))){

      xmlChar *name = xmlGetProp(cur, BAD_CAST "name");

      xmlChar *val = xmlGetProp(cur, BAD_CAST "val");

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_centers")) {

	showcentersp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_nodes")) {

	showmeshp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_node_numbers")) {

	shownodenumbersp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_numbers")) {

	showcellnumbersp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_border_cells")) {

	showbordercellp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_axes")) {

	showcellsaxesp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_strain")) {

	showcellstrainp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_fluxes")) {

	showfluxesp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_walls")) {

	showwallsp = strtobool( (const char *)val );

      }

     /* if (!xmlStrcmp(name, (const xmlChar *)"show_apoplasts")) {

	showapoplastsp = strtobool( (const char *)val );

      }*/

      if (!xmlStrcmp(name, (const xmlChar *)"save_movie_frames")) {

	movieframesp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_only_leaf_boundary")) {

	showboundaryonlyp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"cell_growth")) {

	dynamicscellsp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name,(const xmlChar *)"hide_cells")) {

	hidecellsp = strtobool( (const char *)val ); 

      }

      xmlFree(name);

      xmlFree(val);

    }

    cur=cur->next;

  }

}

void MainBase::Save(const char *fname, const char *format, int sizex, int sizey)

{

  Vector ll,ur;

  mesh.BoundingBox(ll, ur);

  if (QString(fname).isEmpty()) {

    MyWarning::warning("No output filename given. Saving nothing.\n");

    return;

  }

  ll*=Cell::Magnification(); ur*=Cell::Magnification();

  // give the leaf some space

  Vector border = ((ur-ll)/5.);

  if (!QString(format).contains("pdf", Qt::CaseInsensitive)) {

    QImage *image = new QImage(QSize(sizex, sizey), QImage::Format_RGB32);

    image->fill(QColor(Qt::white).rgb());

    QPainter *painter=new QPainter(image);

    canvas.render(painter);

#ifdef QDEBUG

    qDebug() << "Native Image Filename: " << QDir::toNativeSeparators(QString(fname)) << endl;

#endif

      MyWarning::warning("Image not saved successfully. Is the disk full or the extension not recognized?");

    delete painter;

    delete image;

  } else {

    QPrinter pdf(QPrinter::HighResolution);

    pdf.setOutputFileName(fname);

    pdf.setOutputFormat(QPrinter::PdfFormat);

    QPainter painter(&pdf);

    canvas.render(&painter, QRectF(), QRectF(-5000,-5000, 10000, 10000));

    cerr << "Rendering to printer\n";

  }

}

void MainBase::CutSAM()

{

  mesh.CutAwaySAM();

}

/* finis */